Specialized dynamical properties of promiscuous residues revealed by simulated conformational ensembles

The ability to interact with different partners is one of the most important features in proteins. Proteins that bind a large number of partners (hubs) have been often associated with intrinsic disorder. However, many examples exist of hubs with an ordered structure, and evidence of a general mechanism promoting promiscuity in ordered proteins is still elusive. An intriguing hypothesis is that promiscuous binding sites have specific dynamical properties, distinct from the rest of the interface and pre-existing in the protein isolated state. Here, we present the first comprehensive study of the intrinsic dynamics of promiscuous residues in a large protein data set. Different computational methods, from coarse-grained elastic models to geometry-based sampling methods and to full-atom Molecular Dynamics simulations, were used to generate conformational ensembles for the isolated proteins. The flexibility and dynamic correlations of interface residues with a different degree of binding promiscuity were calculated and compared considering side chain and backbone motions, the latter both on a local and on a global scale. The study revealed that (a) promiscuous residues tend to be more flexible than nonpromiscuous ones, (b) this additional flexibility has a higher degree of organization, and (c) evolutionary conservation and binding promiscuity have opposite effects on intrinsic dynamics. Findings on simulated ensembles were also validated on ensembles of experimental structures extracted from the Protein Data Bank (PDB). Additionally, the low occurrence of single nucleotide polymorphisms observed for promiscuous residues indicated a tendency to preserve binding diversity at these positions. A case study on two ubiquitin-like proteins exemplifies how binding promiscuity in evolutionary related proteins can be modulated by the fine-tuning of the interface dynamics. The interplay between promiscuity and flexibility highlighted here can inspire new directions in protein-protein interaction prediction and design methods. © 2013 American Chemical Society

Sex-Specific Growth and Reproductive Dynamics of Red Drum in the Northern Gulf of Mexico

The Red Drum Sciaenops ocellatus stock is heavily targeted in the Gulf of Mexico (GOM) by recreational fishers and supports a small commercial fishery in Mississippi. Despite their popularity, little recent work has been done to describe their life history. In this work, we describe sex‐specific growth and reproductive dynamics of Red Drum collected from the northern GOM from September 2016 through October 2017. We evaluated seven candidate growth models and found that the three‐parameter von Bertalanffy growth function (VBGF) was the best candidate length‐at‐age model. No significant difference in growth between sexes was observed with the three‐parameter VBGF, despite the female‐specific curve having a larger mean asymptotic length than the male‐specific curve. All seven candidate growth models predicted similar mean length‐at‐age estimates, and four of them exhibited significant differences in sex‐specific mean length at age, with females reaching a larger length at age than males after age 5. There was no significant difference between the sex‐specific weight‐at‐length relationships. Red Drum are batch spawners that spawn in northern GOM coastal waters during August and September. We estimated 3.7 d between spawns and 10.5 spawning events per female in 2017. Nearly 20% of fish collected during the spawning season were sexually mature but reproductively inactive, indicating the possibility of skipped spawning. The age at 50% maturity was around 3 years (length at 50% maturity = 670 mm TL) in both sexes, but fish were not spawning capable until age 4.5 (703 mm TL) in males and age 5.8 (840 mm TL) in females. Furthermore, elevated gonadosomatic indices were not observed until around age 5–6. The updated life history information presented in this work helps to address current data limitations and provides critical information for future assessments of Red Drum stocks in the northern GOM

Connectivity and zebra mussel invasion offer short‐term buffering of eutrophication impacts on floodplain lake landscape biodiversity

Aim To investigate if connectivity and zebra mussel (Dreissena polymorpha) occurrence can mitigate effects of eutrophication in a lowland lake landscape. Location Upper Lough Erne, Northern Ireland, UK. Methods Data on environment, macrophytes and invertebrates were assembled for three basins of a large central lake and its satellite floodplain lakes via field surveys and palaeolimnological analyses. Space–time interaction analyses of palaeoecological data were compared pre‐1950 and post‐1950. Multivariate analyses examined how connectivity, environment and zebra mussels influenced contemporary lake communities, and explain their divergence from historical communities in the past. Results Pre‐1950, we found high community variation across sites and low within‐lake variation in macrophytes, but progressive eutrophication accentuated within‐lake community variation after 1950. Partitioning analysis showed larger effects of connectivity than nutrient enrichment on contemporary macrophyte composition, while local effects structured invertebrate communities. Three clusters of lakes were revealed according to variation in macrophyte composition, isolation from the central lake and nutrient enrichment: Group 1– the central lake and six nearby lakes were meso‐eutrophic (TP = 66.7 ± 47.6 μg/L; TN = 0.79 ± 0.41 mg/L) and had the highest zebra mussel abundances and organismal biodiversity; Group 2– Eight eutrophic (TP = 112±36.6 μg/L; TN = 1.25 ± 0.5 mg/L) and connected lakes; Group 3– Seven isolated and hypertrophic (TP = 163.2 ± 101.5 μg/L; TN = 1.55 ± 0.3 mg/L) lakes. Pre‐1950 palaeolimnological data for macrophytes and invertebrates for 5 lakes and a basin in the central lake most resembled extant lake communities of Group 1. However, palaeo‐records revealed that macrophytes and invertebrates subsequently converged towards those of Groups 2 and 3. Main conclusions Our study reveals that the central “mother” lake acts as a hub for preserving biodiversity via shared hydrological connectivity with satellite lakes and high zebra mussel abundances. These may buffer the impoverishing effects of eutrophication and sustain unexpectedly high biodiversity in the short term. Such protective buffering, however, cannot be relied upon indefinitely to conserve biodiversity

Peatland Initiation, Carbon Accumulation, and 2 ka Depth in the James Bay Lowland and Adjacent Regions

Copyright © 2014 University of Colorado at Boulder, Institute of Arctic and Alpine ResearchPeatlands surrounding Hudson and James Bays form the second largest peatland complex in the world and contain major stores of soil carbon (C). This study utilized a transect of eight ombrotrophic peat cores from remote regions of central and northern Ontario to quantify the magnitude and rate of C accumulation since peatland initiation and for the past 2000 calendar years before present (2 ka). These new data were supplemented by 17 millennially resolved chronologies from a literature review covering the Boreal Shield, Hudson Plains, and Taiga Shield bordering Hudson and James Bays. Peatlands initiated in central and northern Ontario by 7.8 ka following deglaciation and isostatic emergence of northern areas to above sea level. Total C accumulated since inception averaged 109.7 ± (std. dev.) 36.2 kg C m–2. Approximately 40% of total soil C has accumulated since 2 ka at an average apparent rate of 20.2 ± 6.9 g C m–2 yr–1. The 2 ka depths correlate significantly and positively with modern gridded climate estimates for mean annual precipitation, mean annual air temperature, growing degree-days > 0 °C, and photosynthetically active radiation integrated over days > 0 °C. There are significantly shallower depths in permafrost peatlands. Vertical peat accumulation was likely constrained by temperature, growing season length, and photosynthetically active radiation over the last 2 ka in the Hudson Bay Lowlands and surrounding regions.US National Science Foundatio

Multiple Data Analyses and Statistical Approaches for Analyzing Data from Metagenomic Studies and Clinical Trials

Metagenomics, also known as environmental genomics, is the study of the genomic content of a sample of organisms (microbes) obtained from a common habitat. Metagenomics and other “omics” disciplines have captured the attention of researchers for several decades. The effect of microbes in our body is a relevant concern for health studies. There are plenty of studies using metagenomics which examine microorganisms that inhabit niches in the human body, sometimes causing disease, and are often correlated with multiple treatment conditions. No matter from which environment it comes, the analyses are often aimed at determining either the presence or absence of specific species of interest in a given metagenome or comparing the biological diversity and the functional activity of a wider range of microorganisms within their communities. The importance increases for comparison within different environments such as multiple patients with different conditions, multiple drugs, and multiple time points of same treatment or same patient. Thus, no matter how many hypotheses we have, we need a good understanding of genomics, bioinformatics, and statistics to work together to analyze and interpret these datasets in a meaningful way. This chapter provides an overview of different data analyses and statistical approaches (with example scenarios) to analyze metagenomics samples from different medical projects or clinical trials

The gut microbiota of Colombians differs from that of Americans, Europeans and Asians

ABSTRACT: The composition of the gut microbiota has recently been associated with health and disease, particularly with obesity. Some studies suggested a higher proportion of Firmicutes and a lower proportion of Bacteroidetes in obese compared to lean people; others found discordant patterns. Most studies, however, focused on Americans or Europeans, giving a limited picture of the gut microbiome. To determine the generality of previous observations and expand our knowledge of the human gut microbiota, it is important to replicate studies in overlooked populations. Thus, we describe here, for the first time, the gut microbiota of Colombian adults via the pyrosequencing of the 16S ribosomal DNA (rDNA), comparing it with results obtained in Americans, Europeans, Japanese and South Koreans, and testing the generality of previous observations concerning changes in Firmicutes and Bacteroidetes with increasing body mass index (BMI). Results: We found that the composition of the gut microbiota of Colombians was significantly different from that of Americans, Europeans and Asians. The geographic origin of the population explained more variance in the composition of this bacterial community than BMI or gender. Concerning changes in Firmicutes and Bacteroidetes with obesity, in Colombians we found a tendency in Firmicutes to diminish with increasing BMI, whereas no change was observed in Bacteroidetes. A similar result was found in Americans. A more detailed inspection of the Colombian dataset revealed that five fiber-degrading bacteria, including Akkermansia, Dialister, Oscillospira, Ruminococcaceae and Clostridiales, became less abundant in obese subjects. Conclusion: We contributed data from unstudied Colombians that showed that the geographic origin of the studied population had a greater impact on the composition of the gut microbiota than BMI or gender. Any strategy aiming to modulate or control obesity via manipulation of this bacterial community should consider this effect

Temporal variability and effect of environmental variables on airborne bacterial communities in an urban area of Northern Italy

Despite airborne microorganisms representing a relevant fraction of atmospheric suspended particles, only a small amount of information is currently available on their abundance and diversity and very few studies have investigated the environmental factors influencing the structure of airborne bacterial communities. In this work, we used quantitative PCR and Illumina technology to provide a thorough description of airborne bacterial communities in the urban area of Milan (Italy). Forty samples were collected in 10-day sampling sessions, with one sessionper season.Themeanbacterialabundancewasabout104 ribosomal operons perm3 of air andwas lower inwinter than in the other seasons. Communitieswere dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and fewproteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales andPseudomonadales).Chloroplastswere abundant in all samples. Ahigher abundanceof Actinobacteridae,which are typical soil-inhabiting bacteria, and a lower abundance of chloroplasts in samples collected on cold days were observed. The variation in community composition observed within seasons was comparable to that observed between seasons, thus suggesting that airborne bacterial communities showlarge temporal variability, even between consecutive days. The structure of airborne bacterial communities therefore suggests that soil and plants are the sources which contribute most to the airborne communities of Milan atmosphere, but the structure of the bacterial community seems to depend mainly on the source of bacteria that predominates in a given period of time